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Old 05-24-2013, 07:17 AM   #1
Lyn Hsiong
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Location: China

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Default how to merge contiguous blast hsps! (-m 8 tab)

Hi, guys!

I performed blastx (-m 8) using a query file of many sequences, and for each target sequence, the output contains many fragmental hsps of significance, and these hsps have overlap positions or not.

so, how can i merge those closely related hsps into one via setting a flanking value (e.g <300bp) when these hsps match the same subject (different regions).

In the attached figure, I want to transform the upper results to the lower ones

Thanks in advance!




Transform

scaffold16:1661-2239(+) gi|471236998|ref|YP_007641386.1| 50.00 122 52 3 225 578 603 719 2e-53 126
scaffold16:1661-2239(+) gi|471236998|ref|YP_007641386.1| 75.00 76 19 0 1 228 528 603 2e-53 108
scaffold16:1661-2239(+) gi|333951646|gb|AEG25349.1| 52.10 119 54 2 225 578 604 720 7e-53 124
scaffold16:1661-2239(+) gi|333951646|gb|AEG25349.1| 77.63 76 17 0 1 228 529 604 7e-53 109
scaffold28:2776872-2777385(-) gi|327335359|gb|AEA49877.1| 70.18 57 17 0 173 343 554 610 3e-30 90.5
scaffold28:2776872-2777385(-) gi|327335359|gb|AEA49877.1| 72.22 54 15 0 1 162 497 550 3e-30 67.0

To

scaffold16:1661-2239(+) gi|471236998|ref|YP_007641386.1| . . . . 1 578 . . 2e-53 234
scaffold16:1661-2239(+) gi|333951646|gb|AEG25349.1| . . . . 1 578 . . 7e-53 233
scaffold28:2776872-2777385(-) gi|327335359|gb|AEA49877.1| . . . . 1 343 . . 3e-30 157.0
Attached Images
File Type: png blast.png (10.0 KB, 4 views)

Last edited by Lyn Hsiong; 05-24-2013 at 07:19 AM.
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Old 06-06-2013, 01:31 AM   #2
Torst
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Location: The University of Melbourne, AUSTRALIA

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Default

If you parse with Bio::Perl, you can use the tile_hsps() function in the GenericHit module and use the coordinates it provides.
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Old 06-06-2013, 06:24 PM   #3
Lyn Hsiong
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Quote:
Originally Posted by Torst View Post
If you parse with Bio::Perl, you can use the tile_hsps() function in the GenericHit module and use the coordinates it provides.
Thank you for your reply!
Do you mean the function Bio::Search::SearchUtils::tile_hsps($hit)?
I have checked the usage, but I am afraid that I still need a simple practical example, even if only several lines code.

Did you use that function before? It is kind of you to give me a hand, thanks a lot!
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